1887

Abstract

A red-pigmented, bacteriochlorophyll (BChl) -producing strain, AP64, was isolated previously from the freshwater Swan Lake located in the western Gobi Desert. Based on its 16S rRNA gene sequence identity (96.1 %) to the type strain T-27, the new isolate was tentatively classified as a member of the bacterial phylum . Here, we report its formal description and polyphasic characterization. Strain AP64 grew best on agar media under 9.8–15.2 % atmospheric oxygen. The cells were rods, dividing by symmetrical or asymmetrical binary fission. Budding structures were also observed. Its genomic DNA G+C content was 64.4 % (from the draft genome sequence). Phylogenetic analysis based on the 16S rRNA gene sequence clearly separated AP64 from related species. Its genotypic differentiation from phylogenetically close relatives was further supported by performing DNA–DNA hybridization and calculating average nucleotide identity, whereas the high percentage (67.3 %) of shared conserved proteins between strain AP64 and T-27 supports the classification of the two strains into the same genus. Strain AP64 contained C, C and Cω9 as predominant fatty acids. The main respiratory quinone was menaquinone 8 (MK-8). The most distinctive feature of strain AP64 was the presence of fully functional purple bacterial photosynthetic reaction centres. The main CO-fixation pathways were absent. Strain AP64 was capable of growth and BChl production in constant darkness. Thus, strain AP64 is a facultatively photoheterotrophic organism. It represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is AP64 ( = DSM 29774 = MCCC 1K00454). Emended descriptions of the genus and are also provided.

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2015-08-01
2024-11-06
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References

  1. Auch A.F., von Jan M., Klenk H.P., Göker M. ( 2010;). Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2 117134 [View Article] [PubMed] .
    [Google Scholar]
  2. Aziz R.K., Bartels D., Best A.A., DeJongh M., Disz T., Edwards R.A., Formsma K., Gerdes S., Glass E.M., other authors. ( 2008;). The rast Server: rapid annotations using subsystems technology. BMC Genomics 9 75 [View Article] [PubMed] .
    [Google Scholar]
  3. Darling A.E., Mau B., Perna N.T. ( 2010;). progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5 e11147 [View Article] [PubMed] .
    [Google Scholar]
  4. DeBruyn J.M., Nixon L.T., Fawaz M.N., Johnson A.M., Radosevich M. ( 2011;). Global biogeography and quantitative seasonal dynamics of Gemmatimonadetes in soil. Appl Environ Microbiol 77 62956300 [View Article] [PubMed] .
    [Google Scholar]
  5. DeBruyn J.M., Fawaz M.N., Peacock A.D., Dunlap J.R., Nixon L.T., Cooper K.E., Radosevich M. ( 2013;). Gemmatirosa kalamazoonesis gen. nov., sp. nov., a member of the rarely-cultivated bacterial phylum Gemmatimonadetes . J Gen Appl Microbiol 59 305312 [View Article] [PubMed] .
    [Google Scholar]
  6. DeSantis T.Z., Hugenholtz P., Larsen N., Rojas M., Brodie E.L., Keller K., Huber T., Dalevi D., Hu P., Andersen G.L. ( 2006;). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with arb . Appl Environ Microbiol 72 50695072 [View Article] [PubMed] .
    [Google Scholar]
  7. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. ( 2007;). DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57 8191 [View Article] [PubMed] .
    [Google Scholar]
  8. Hanada S., Sekiguchi Y. ( 2014;). The phylum Gemmatimonadetes. . In The Prokaryotes , 4th edn. vol. 11, pp. 677681. Edited by Rosenberg E, DeLong E. F, Lory S, Stackebrandt E, Thompson F. Berlin, Heidelberg: Springer;.
    [Google Scholar]
  9. Kainz M., Lucotte M., Parrish C.C. ( 2002;). Methyl mercury in zooplankton – the role of size, habitat, and food quality. Can J Fish Aquat Sci 59 16061615 [View Article].
    [Google Scholar]
  10. Kamagata Y. ( 2010;). Phylum XXI. Gemmatimonadetes Zhang, Sekiguchi, Hanada, Hugenholtz, Kim, Kamagata and Nakamura 2003, 1161VP . [View Article] In Bergey's Manual of Systematic Bacteriology , 2nd edn. vol. 4, pp. 781784. Edited by Krieg N. R, Staley J. T, Brown D. R, Hedlund B. P, Paster B. J, Ward N. L, Ludwig W, Whitman W. B. New York: Springer;.
    [Google Scholar]
  11. Kim O.S., Cho Y.J., Lee K., Yoon S.H., Kim M., Na H., Park S.C., Jeon Y.S., Lee J.H., other authors. ( 2012;). Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62 716721 [View Article] [PubMed] .
    [Google Scholar]
  12. Koblížek M., Mlčoušková J., Kolber Z., Kopecký J. ( 2010;). On the photosynthetic properties of marine bacterium COL2P belonging to Roseobacter clade. Arch Microbiol 192 4149 [View Article] [PubMed] .
    [Google Scholar]
  13. Konstantinidis K.T., Tiedje J.M. ( 2005;). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102 25672572 [View Article] [PubMed] .
    [Google Scholar]
  14. Lukeš M., Procházková L., Shmidt V., Nedbalová L., Kaftan D. ( 2014;). Temperature dependence of photosynthesis and thylakoid lipid composition in the red snow alga Chlamydomonas cf. nivalis (Chlorophyceae). FEMS Microbiol Ecol 89 303315 [View Article] [PubMed] .
    [Google Scholar]
  15. Meier-Kolthoff J.P., Auch A.F., Klenk H.P., Göker M. ( 2013;). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14 60 [View Article] [PubMed] .
    [Google Scholar]
  16. Potts M. ( 1994;). Desiccation tolerance of prokaryotes. Microbiol Rev 58 755805 [PubMed].
    [Google Scholar]
  17. Pruesse E., Peplies J., Glöckner F.O. ( 2012;). sina: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28 18231829 [View Article] [PubMed] .
    [Google Scholar]
  18. Qin Q.L., Xie B.B., Zhang X.Y., Chen X.L., Zhou B.C., Zhou J., Oren A., Zhang Y.Z. ( 2014;). A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 196 22102215 [View Article] [PubMed] .
    [Google Scholar]
  19. Richter M., Rosselló-Móra R. ( 2009;). Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106 1912619131 [View Article] [PubMed] .
    [Google Scholar]
  20. Takaichi S., Maoka T., Takasaki K., Hanada S. ( 2010;). Carotenoids of Gemmatimonas aurantiaca (Gemmatimonadetes): identification of a novel carotenoid, deoxyoscillol 2-rhamnoside, and proposed biosynthetic pathway of oscillol 2,2′-dirhamnoside. Microbiology 156 757763 [View Article] [PubMed] .
    [Google Scholar]
  21. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. ( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30 27252729 [View Article] [PubMed] .
    [Google Scholar]
  22. Zeng Y., Feng F., Medová H., Dean J., Koblížek M. ( 2014;). Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. Proc Natl Acad Sci U S A 111 77957800 [View Article] [PubMed] .
    [Google Scholar]
  23. Zhang H., Sekiguchi Y., Hanada S., Hugenholtz P., Kim H., Kamagata Y., Nakamura K. ( 2003;). Gemmatimonas aurantiaca gen. nov., sp. nov., a Gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov. Int J Syst Evol Microbiol 53 11551163 [View Article] [PubMed] .
    [Google Scholar]
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